Endophytic and ectophytic potato-associated bacterial communities differ in structure and antagonistic function against plant pathogenic fungi

Analysis of endophytic bacterial diversity in seeds of different genotypes of cotton and the suppression of Verticillium wilt pathogen infection by a synthetic microbial community

BACKGROUND

In agricultural production, fungal diseases significantly impact the yield and quality of cotton (Gossypium spp.) with Verticillium wilt posing a particularly severe threat.

RESULTS

This study is focused on investigating the effectiveness of endophytic microbial communities present in the seeds of disease-resistant cotton genotypes in the control of cotton Verticillium wilt. The technique of 16S ribosomal RNA (16S rRNA) amplicon sequencing identified a significant enrichment of the Bacillus genus in the resistant genotype Xinluzao 78, which differed from the endophytic bacterial community structure in the susceptible genotype Xinluzao 63. Specific enriched strains were isolated and screened from the seeds of Xinluzao 78 to further explore the biological functions of seed endophytes. A synthetic microbial community (SynCom) was constructed using the broken-rod model, and seeds of the susceptible genotype Xinluzao 63 in this community that had been soaked with the SynCom were found to significantly control the occurrence of Verticillium wilt and regulate the growth of cotton plants. Antibiotic screening techniques were used to preliminarily identify the colonization of strains in the community. These techniques revealed that the strains can colonize plant tissues and occupy ecological niches in cotton tissues through a priority effect, which prevents infection by pathogens.

CONCLUSION

This study highlights the key role of seed endophytes in driving plant disease defense and provides a theoretical basis for the future application of SynComs in agriculture.

Plant endophytes: unveiling hidden applications toward agro-environment sustainability

Endophytic microbes are plant-associated microorganisms that reside in the interior tissue of plants without causing damage to the host plant. Endophytic microbes can boost the availability of nutrient for plant by using a variety of mechanisms such as fixing nitrogen, solubilizing phosphorus, potassium, and zinc, and producing siderophores, ammonia, hydrogen cyanide, and phytohormones that help plant for growth and protection against various abiotic and biotic stresses. The microbial endophytes have attained the mechanism of producing various hydrolytic enzymes such as cellulase, pectinase, xylanase, amylase, gelatinase, and bioactive compounds for plant growth promotion and protection. The efficient plant growth promoting endophytic microbes could be used as an alternative of chemical fertilizers for agro-environmental sustainability. Endophytic microbes belong to different phyla including Euryarchaeota, Ascomycota, Basidiomycota, Mucoromycota, Firmicutes, Proteobacteria, and Actinobacteria. The most pre-dominant group of bacteria belongs to Proteobacteria including α-, β-, γ-, and δ-Proteobacteria. The least diversity of the endophytic microbes have been revealed from Bacteroidetes, Deinococcus-Thermus, and Acidobacteria. Among reported genera, Achromobacter, Burkholderia, Bacillus, Enterobacter, Herbaspirillum, Pseudomonas, Pantoea, Rhizobium, and Streptomyces were dominant in most host plants. The present review deals with plant endophytic diversity, mechanisms of plant growth promotion, protection, and their role for agro-environmental sustainability. In the future, application of endophytic microbes have potential role in enhancement of crop productivity and maintaining the soil health in sustainable manner.

Filtration effect of Cordyceps chanhua mycoderm on bacteria and its transport function on nitrogen

IMPORTANCE

During the natural growth of Cordyceps chanhua, it will form a mycoderm structure specialized from hyphae. We found that the bacterial membrane of C. chanhua not only filters environmental bacteria but also absorbs and transports nitrogen elements inside and outside the body of C. chanhua. These findings are of great significance for understanding the stable mechanism of the internal microbial community maintained by C. chanhua and how C. chanhua maintains its own nutritional balance. In addition, this study also enriched our understanding of the differences in bacterial community composition and related bacterial community functions of C. chanhua at different growth stages, which is of great value for understanding the environmental adaptation mechanism, the element distribution network, and the changing process of symbiotic microbial system after Cordyceps fungi infected the host. At the same time, it can also provide a theoretical basis for some important ecological imitation cultivation technology of Cordyceps fungi.

Harnessing fungal endophytes for natural management: a biocontrol perspective

In the ever-evolving realm of agriculture, the convoluted interaction between plants and microorganisms have assumed paramount significance. Fungal endophytes, once perceived as mere bystanders within plant tissues, have now emerged as dynamic defenders of plant health. This comprehensive review delves into the captivating world of fungal endophytes and their multifaceted biocontrol mechanisms. Exploring their unique ability to coexist with their plant hosts, fungal endophytes have unlocked a treasure trove of biological weaponry to fend off pathogens and enhance plant resilience. From the synthesis of bioactive secondary metabolites to intricate signaling pathways these silent allies are masters of biological warfare. The world of fungal endophytes is quite fascinating as they engage in a delicate dance with the plant immune system, orchestrating a symphony of defense that challenges traditional notions of plant-pathogen interactions. The journey through the various mechanisms employed by these enigmatic endophytes to combat diseases, will lead to revelational understanding of sustainable agriculture. The review delves into cutting-edge research and promising prospects, shedding light on how fungal endophytes hold the key to biocontrol and the reduction of chemical inputs in agriculture. Their ecological significance, potential for bioprospecting and avenues for future research are also explored. This exploration of the biocontrol mechanisms of fungal endophytes promise not only to enrich our comprehension of plant-microbe relationships but also, to shape the future of sustainable and ecofriendly agricultural practices. In this intricate web of life, fungal endophytes are indeed the unsung heroes, silently guarding our crops and illuminating a path towards a greener, healthier tomorrow.

Salt tolerance of endophytic root bacteria and their effects on seed germination and viability on tomato plants

Salinity is one of the most brutal environmental factors limiting the productivity of agricultural lands worldwide. It is considered that the salinity may be one of the important reasons for the low yield in Iğdır of the tomato plants, which is medium resistant (3-5 dS.m-1) among vegetables. Eco-friendly techniques such as endophytic root bacteria treatments (ERB) are needed to restore saline soils to agriculture and also to increase the yield of tomatoes. Endophytic bacteria colonizing the inside of plants increase plant growth by various mechanisms and also mitigate the adverse effects of biotic and abiotic stresses on plants. In this study, endophytic bacteria were isolated from the roots of tomato plants exposed to salt stress. Then, these isolates' tolerance levels to different NaCl (0, 0.1, 0.2, 0.4, 0.8 M) concentrations and their potential to promote plant growth (PGP) traits were determined. It was recorded that 14.8% of the isolates whose salt tolerance was tested were highly tolerant to NaCl and 18.5% were highly susceptible. The tested ERB isolates exhibited typical PGP characteristics such as siderophore production (4-30 mm diameter), phosphate solubilizing activity (6-16 mm diameter), and IAA production activity (24.9-171.6 µg/ml). Moreover, it was determined that the nitrogen fixation potential is high 55.7% of the isolates tested, and 11.1% low. In addition, the effects of ERB treatments on germination and vigor index in two tomato cultivars under standard and saline conditions in the lab were evaluated. Some ERB isolates in tomato plants under standard and saline conditions increased seed viability, hypocotyl length, root length, and seedling fresh weight, and also accelerated germination.

The toxicological spectrum of the Bacillus cereus toxin cereulide points towards niche-specific specialisation

Most microbes share their environmental niches with very different forms of life thereby engaging in specialised relationships to enable their persistence. The bacterium Bacillus cereus occurs ubiquitously in the environment with certain strain backgrounds causing foodborne and opportunistic infections in humans. The emetic lineage of B. cereus is capable of producing the toxin cereulide, which evokes emetic illnesses. Although food products favouring the accumulation of cereulide are known, the ecological role of cereulide and the environmental niche of emetic B. cereus remain elusive. To better understand the ecology of cereulide-producing B. cereus, we systematically assayed the toxicological spectrum of cereulide on a variety of organisms belonging to different kingdoms. As cereulide is a potassium ionophore, we further tested the effect of environmental potassium levels on the action of cereulide. We found that adverse effects of cereulide exposure are species-specific, which can be exacerbated with increased environmental potassium. Additionally, we demonstrate that cereulide is produced within an insect cadaver indicating its potential ecological function for a saprophytic lifestyle. Collectively, distinct cereulide susceptibilities of other organisms may reflect its role in enabling competitive niche specialization of emetic B. cereus.

Beneficial microbial consortium improves winter rye performance by modulating bacterial communities in the rhizosphere and enhancing plant nutrient acquisition

The beneficial effect of microbial consortium application on plants is strongly affected by soil conditions, which are influenced by farming practices. The establishment of microbial inoculants in the rhizosphere is a prerequisite for successful plant-microorganism interactions. This study investigated whether a consortium of beneficial microorganisms establishes in the rhizosphere of a winter crop during the vegetation period, including the winter growing season. In addition, we aimed for a better understanding of its effect on plant performance under different farming practices. Winter rye plants grown in a long-time field trial under conventional or organic farming practices were inoculated after plant emergence in autumn with a microbial consortium containing Pseudomonas sp. (RU47), Bacillus atrophaeus (ABi03) and Trichoderma harzianum (OMG16). The density of the microbial inoculants in the rhizosphere and root-associated soil was quantified in autumn and the following spring. Furthermore, the influence of the consortium on plant performance and on the rhizosphere bacterial community assembly was investigated using a multidisciplinary approach. Selective plating showed a high colonization density of individual microorganisms of the consortium in the rhizosphere and root-associated soil of winter rye throughout its early growth cycle. 16S rRNA gene amplicon sequencing showed that the farming practice affected mainly the rhizosphere bacterial communities in autumn and spring. However, the microbial consortium inoculated altered also the bacterial community composition at each sampling time point, especially at the beginning of the new growing season in spring. Inoculation of winter rye with the microbial consortium significantly improved the plant nutrient status and performance especially under organic farming. In summary, the microbial consortium showed sufficient efficacy throughout vegetation dormancy when inoculated in autumn and contributed to better plant performance, indicating the potential of microbe-based solutions in organic farming where nutrient availability is limited.

Schizotrophic Sclerotinia sclerotiorum-Mediated Root and Rhizosphere Microbiome Alterations Activate Growth and Disease Resistance in Wheat

Sclerotinia sclerotiorum, a widespread pathogen of dicotyledons, can grow endophytically in wheat, providing protection against Fusarium head blight and stripe rust and enhancing wheat yield. In this study, we found that wheat seed treatment with strain DT-8, infected with S. sclerotiorum hypovirulence-associated DNA virus 1 (SsHADV-1) and used as a "plant vaccine" for brassica protection, could significantly increase the diversity of the fungal and bacterial community in rhizosphere soil, while the diversity of the fungal community was obviously decreased in the wheat root. Interestingly, the relative abundance of potential plant growth-promoting rhizobacteria (PGPR) and biocontrol agents increased significantly in the DT-8-treated wheat rhizosphere soil. These data might be responsible for wheat growth promotion and disease resistance. These results may provide novel insights for understanding the interaction between the schizotrophic microorganism and the microbiota of plant roots and rhizosphere, screening and utilizing beneficial microorganisms, and further reducing chemical pesticide utilization and increasing crop productivity. IMPORTANCE Fungal pathogens are seriously threatening food security and natural ecosystems; efficient and environmentally friendly control methods are essential to increase world crop production. S. sclerotiorum, a widespread pathogen of dicotyledons, can grow endophytically in wheat, providing protection against Fusarium head blight and stripe rust and enhancing wheat yield. In this study, we discovered that S. sclerotiorum treatment increased the diversity of the soil fungal and bacterial community in rhizosphere soil, while the diversity of the fungal community was obviously decreased in the wheat root. More importantly, the relative abundance of potential PGPR and bio-control agents increased significantly in the S. sclerotiorum-treated wheat rhizosphere soil. The importance of this work is that schizotrophic S. sclerotiorum promotes wheat growth and enhances resistance against fungal diseases via changes in the structure of the root and rhizosphere microbiome.

Deciphering the antimicrobial activity of multifaceted rhizospheric biocontrol agents of solanaceous crops viz., Trichoderma harzianum MC2, and Trichoderma harzianum NBG

The Solanaceae family is generally known to be the third most economically important plant taxon, but also harbors a host of plant pathogens. Diseases like wilt and fruit rot of solanaceous crops cause huge yield losses in the field as well as in storage. In the present study, eight isolates of Trichoderma spp. were obtained from rhizospheric micro-flora of three solanaceous crops: tomato, brinjal, and chili plants, and were subsequently screened for pre-eminent biocontrol activity against three fungal (Fusarium oxysporum f. sp. lycopersicum, Colletotrichum gloeosporioides, and Rhizoctonia solani) and one bacterial (Ralstonia solanacearum) pathogen. Morphological, ITS, and tef1α marker-based molecular identification revealed eight isolates were different strains of Trichoderma. Seven isolates were distinguished as T. harzianum while one was identified as T. asperellum. In vitro antagonistic and biochemical assays indicated significant biocontrol activity governed by all eight isolates. Two fungal isolates, T. harzianum MC2 and T. harzianum NBG were further evaluated to decipher their best biological control activity. Preliminary insights into the secondary metabolic profile of both isolates were retrieved by liquid chromatography-mass spectrometry (LC-MS). Further, a field experiment was conducted with the isolates T. harzianum MC2 and T. harzianum NBG which successfully resulted in suppression of bacterial wilt disease in tomato. Which possibly confer biocontrol properties to the identified isolates. The efficacy of these two strains in suppressing bacterial wilt and promoting plant growth in the tomato crop was also tested in the field. The disease incidence was significantly reduced by 47.50% and yield incremented by 54.49% in plants treated in combination with both the bioagents. The results of scanning electron microscopy were also in consensus with the in planta results. The results altogether prove that T. harzianum MC2 and T. harzianum NBG are promising microbes for their prospective use in agricultural biopesticide formulations.

Management of Black Root Disease-Causing Fungus Fusarium solani CRP1 by Endophytic Bacillus siamensis CNE6 through Its Metabolites and Activation of Plant Defense Genes

Black root rot disease of Cicer arietinum L. is accountable for substantial loss in chickpea production worldwide. Endophytic Bacillus siamensis CNE6 has previously shown multifaceted plant growth-promoting, broad-spectrum antifungal, and chickpea plant-colonizing potential. In the present study, the strain Bacillus siamensis CNE6 was used for controlling black root rot disease caused by Fusarium solani CRP1 in chickpea. CNE6 showed strong antagonistic potential against CRP1 both in vivo and in vitro. Scanning electron microscopic studies indicated cellular deformation of CRP1 due to production of β-glucanase, protease, and other secondary metabolites. A total of five compounds were detected from the cell-free supernatant (CFS) of the ethyl acetate (EA) fraction of CNE6 through gas chromatography-mass spectrometry analysis. A confocal microscopic study demonstrated strong inhibition of biofilm formation of the pathogen CRP1 by the EA fraction of CFS of CNE6. Molecular docking analysis revealed that one compound, (2E)-6-methoxy-2-[(4-methoxyphenyl)methylidene]-2,3-dihydro-1-benzofuran-3-one, may inhibit the activity of lanosterol 14-alpha demethylase, which is involved in ergosterol biosynthesis and beta-tubulin assembling. In vivo experiments also showed the efficacy of CNE6 for increasing chickpea growth as well as upregulation of four defense genes (CHI1, PAMP, PR2B, and TF1082) upon pathogenic challenge. Thus, our results strongly suggest a positive role for CNE6 as a prospective biocontrol agent for combating Fusarium solani in chickpea. IMPORTANCE The present work was undertaken to explore an effective biocontrol agent against the destructive black root rot disease of chickpea. We have used an efficient bacterial endophyte, CNE6, which can colonize in the chickpea root system, produce secondary metabolites and enzymes to degrade pathogenic cellular integrity, inhibit pathogenic establishment by rupturing biofilm formation, and induce host immunity upon treatment. Interaction of the bacterial metabolite was also observed with lanosterol 14-alpha demethylase, which is an important component in fungal membrane functioning. Being an endophyte, Bacillus siamensis CNE6 fulfills a suitable criterion as a biocontrol agent to control black root rot disease in chickpea and has huge prospects for use commercially.

Characterization of the Mechanism of Action of Serratia rubidaea Mar61-01 against Botrytis cinerea in Strawberries

Several bacterial strains belonging to Serratia spp. possess biocontrol capability, both against phytopathogens and human pathogenic species, thanks to the production of secondary metabolites, including as a red-pink, non-diffusible pigment, 2-methyl-3-pentyl-6-methoxyprodiginine (prodigiosin). Botrytis cinerea is the causal agent of gray mold, which is an economically relevant disease of many crops worldwide. Gray mold is normally controlled by chemical fungicides, but the environmental and health concerns about the overuse of pesticides call for environmentally friendly approaches, such as the use of biocontrol agents. In this study, the efficacy of a specific strain of Serratia rubidaea (Mar61-01) and its metabolite prodigiosin were assessed against B. cinerea under in vitro and in vivo conditions. This strain was effective against B. cinerea, and the effect of prodigiosin was confirmed under in vitro and in vivo conditions. The strain suppressed mycelial growth of B. cinerea (71.72%) in the dual-culture method. The volatile compounds produced by the strain inhibited mycelial growth and conidia germination of B. cinerea by 65.01% and 71.63%, respectively. Efficacy of prodigiosin produced by S. rubidaea Mar61-01 on mycelial biomass of B. cinerea was 94.15% at the highest concentration tested (420 µg/mL). The effect of prodigiosin on plant enzymes associated with induction of resistance was also studied, indicating that the activity of polyphenol oxidase (PPO), superoxide dismutase (SOD) and phenylalanine ammonia lyase (PAL) were increased when prodigiosin was added to the B. cinerea inoculum on strawberry fruits, while catalase (CAT) and peroxidase (POD) did not change. In addition, the volatile organic compounds (VOCs) produced by S. rubidaea Mar61-01 reduced mycelial growth and inhibited conidial germination of B. cinerea in vitro. The findings confirmed the relevant role of prodigiosin produced by S. rubidaea Mar61-01 in the biocontrol of B. cinerea of strawberries, but also indicate that there are multiple mechanisms of action, where the VOCs produced by the bacterium and the plant-defense reaction may contribute to the control of the phytopathogen. Serratia rubidaea Mar61-01 could be a suitable strain, both to enlarge our knowledge about the potential of Serratia as a biocontrol agent of B. cinerea and to develop new biofungicides to protect strawberries in post-harvest biocontrol.

Endophytic Pseudomonas sp. from Agave palmeri Participate in the Rhizophagy Cycle and Act as Biostimulants in Crop Plants

Plant growth-promoting bacteria are generating increasing interest in the agricultural industry as a promising alternative to traditional chemical fertilizers; however, much of the focus has been on rhizosphere bacteria. Bacterial endophytes are another promising source of plant growth-promoting bacteria, and though many plants have already been prospected for beneficial microbes, desert plants have been underrepresented in such studies. In this study, we show the growth-promoting potential of five strains of endophytic Pseudomonas sp. isolated from Agave palmeri, an agave from the Sonoran Desert. When inoculated onto Kentucky bluegrass, clover, carrot, coriander, and wheat, endophytic Pseudomonas sp. increased seedling root lengths in all hosts and seedling shoot lengths in Kentucky bluegrass, carrot, and wheat. Transformation of the Pseudomonas sp. strain P3AW to express the fluorescent protein mCherry revealed that Pseudomonas sp. becomes endophytic in non-native hosts and participates in parts of the rhizophagy cycle, a process by which endophytic bacteria cycle between the soil and roots, bringing in nutrients from the soil which are then extracted through reactive oxygen-mediated bacterial degradation in the roots. Tracking of the Pseudomonas sp. strain P3AW also provided evidence for a system of endophyte, or endophyte cell content, transport via the vascular bundle. These results provide further evidence of the rhizophagy cycle in plants and how it relates to growth promotion in plants by biostimulant bacteria.

Trichoderma reesei as an elicitor triggers defense responses in tea plant and delays gray blight symptoms

Gray blight caused by Pestalotiopsis-like species is a major disease of tea crop worldwide including India, causes significant losses in tea production. Management of disease using fungal biocontrol agents is considered an alternative eco-friendly approach to synthetic fungicides. The present study explores the efficacy of Trichoderma reesei in the gray blight management in tea crop and activation of defense related enzymes against gray blight pathogen by developing a tri-trophic interaction system. Out of 16 isolates of Trichoderma species screened in laboratory against Pseudopestalotiopsis theae, a gray blight pathogen, isolate TRPATH01 had highest antagonistic activity (81.2%) against Ps. theae and was found to produce inhibitory volatile and non-volatile metabolites. Based on ITS and TEF-1 alpha sequencing, the isolate TRPATH01 was recognised as T. reesei. The methanolic extract of T. reesei was also found effective against Ps. theae at 200 μg/mL also confirmed presence of highest volatile compounds. The isolate also produced hydrolytic enzymes such as chitinase, cellulase, protease, and lipase. Under nursery conditions, 2% and 5% concentrations with 2 × 10⁶ conidia/ml of T. reesei were able to reduce 67.5% to 75.0% of disease severity over pathogen inoculated controls. Moreover, compared with positive and negative controls, T. reesei -treated tea plants showed increased shoot height, stem diameter, shoot and root fresh weight at 45 days after inoculation. Principal component analysis capturing 97.1% phenotypic variations, which revealed that the tea plants co-inoculated with Ps. theae and T. reesei exhibited significantly upregulated accumulation of defensive enzymes viz., polyphenol oxidase, peroxidase, phenylalanine ammonia lyase, phenolics, β-1, 3-glucanase, and chitinase when compared to both controls. Hence, T. reesei could provide an eco-friendly and viable mitigation option for gray blight in tea gardens by inducing defense-related enzymes.

Bacillus spp.-Mediated Growth Promotion of Rice Seedlings and Suppression of Bacterial Blight Disease under Greenhouse Conditions

Rice (Oryza sativa L.) is a major cereal and staple food crop worldwide, and its growth and production are affected by several fungal and bacterial phytopathogens. Bacterial blight (BB) is one of the world's most devastating rice diseases, caused by Xanthomonas oryzae pv. oryzae (Xoo). In the current study, Bacillus atrophaeus FA12 and B. cabrialesii FA26 were isolated from the rice rhizosphere and characterized as having broad-range antifungal and antibacterial activities against various phytopathogens, including Xoo. In addition, the selected strains were further evaluated for their potent rice growth promotion and suppression efficacy against BB under greenhouse conditions. The result shows that FA12 and FA26, applied as seed inoculants, significantly enhanced the vigor index of rice seedlings by 78.89% and 108.70%, respectively. Suppression efficacy against BB disease by FA12 and FA26 reached up to 59.74% and 54.70%, respectively, in pot experiments. Furthermore, MALDI-TOF MS analysis of selected strains revealed the masses ranged from m/z 1040 to 1540, representing that iturins and fengycin are the major antimicrobial compounds in the crude extracts, which might have beneficial roles in rice defence responses against BB. In conclusion, FA12 and FA26 possess broad-range antagonistic activity and have the capability to promote plant growth traits. More importantly, applying these strains has a high potential for implementing eco-friendly, cost-effective, and sustainable management practices for BB disease.

Novel Approaches for Sustainable Horticultural Crop Production: Advances and Prospects

Reduction of plant growth, yield and quality due to diverse environmental constrains along with climate change significantly limit the sustainable production of horticultural crops. In this review, we highlight the prospective impacts that are positive challenges for the application of beneficial microbial endophytes, nanomaterials (NMs), exogenous phytohormones strigolactones (SLs) and new breeding techniques (CRISPR), as well as controlled environment horticulture (CEH) using artificial light in sustainable production of horticultural crops. The benefits of such applications are often evaluated by measuring their impact on the metabolic, morphological and biochemical parameters of a variety of cultures, which typically results in higher yields with efficient use of resources when applied in greenhouse or field conditions. Endophytic microbes that promote plant growth play a key role in the adapting of plants to habitat, thereby improving their yield and prolonging their protection from biotic and abiotic stresses. Focusing on quality control, we considered the effects of the applications of microbial endophytes, a novel class of phytohormones SLs, as well as NMs and CEH using artificial light on horticultural commodities. In addition, the genomic editing of plants using CRISPR, including its role in modulating gene expression/transcription factors in improving crop production and tolerance, was also reviewed.

Soil and Soilless Tomato Cultivation Promote Different Microbial Communities That Provide New Models for Future Crop Interventions

The cultivation of soilless tomato in greenhouses has increased considerably, but little is known about the assembly of the root microbiome compared to plants grown in soil. To obtain such information, we constructed an assay in which we traced the bacterial and fungal communities by amplicon-based metagenomics during the cultivation chain from nursery to greenhouse. In the greenhouse, the plants were transplanted either into agricultural soil or into coconut fiber bags (soilless). At the phylum level, bacterial and fungal communities were primarily constituted in all microhabitats by Proteobacteria and Ascomycota, respectively. The results showed that the tomato rhizosphere microbiome was shaped by the substrate or soil in which the plants were grown. The microbiome was different particularly in terms of the bacterial communities. In agriculture, enrichment has been observed in putative biological control bacteria of the genera Pseudomonas and Bacillus and in potential phytopathogenic fungi. Overall, the study describes the different shaping of microbial communities in the two cultivation methods.

Secretion of poly-γ-glutamic acid by Bacillus atrophaeus NX-12 enhanced its root colonization and biocontrol activity

Bacilli are used as biocontrol agents (BCAs) against phytopathogens and most of them can produce poly-γ-glutamic acid (γ-PGA) as one of the major extracellular polymeric substances (EPSs). However, the role of γ-PGA in plant biocontrol is still unclear. In this study, Bacillus atrophaeus NX-12 (γ-PGA yield: 16.8 g/l) was screened, which formed a strong biofilm and has been proved to be a promising BCA against Cucumber Fusarium wilt. Then, the γ-PGA synthesis gene cluster pgsBCA was knocked out by CRISPR-Cas9n. Interestingly, the antifungal ability of γ-PGA synthetase-deficient strain NX-12Δpgs (γ-PGA yield: 1.65 g/l) was improved in vitro, while the biocontrol ability of NX-12Δpgs was greatly diminished in situ. Data proved that γ-PGA produced by NX-12 contributes to the biofilm formation and rhizosphere colonization, which effectively improved biocontrol capability. Taken together, these findings prove that the mechanism of γ-PGA promotes the colonization of NX-12 and thus assists in controlling plant diseases, which highlight the key role of γ-PGA produced by BCA in biocontrol.

The Brassica napus seed microbiota is cultivar-specific and transmitted via paternal breeding lines

Seed microbiota influence germination and plant health and have the potential to improve crop performance, but the factors that determine their structure and functions are still not fully understood. Here, we analysed the impact of plant‐related and external factors on seed endophyte communities of 10 different oilseed rape (Brassica napus L.) cultivars from 26 field sites across Europe. All seed lots harboured a high abundance and diversity of endophytes, which were dominated by six genera: Ralstonia, Serratia, Enterobacter, Pseudomonas, Pantoea, and Sphingomonas. The cultivar was the main factor explaining the variations in bacterial diversity, abundance and composition. In addition, the latter was significantly influenced by diverse biotic and abiotic factors, for example host germination rates and disease resistance against Plasmodiophora brassicae. A set of bacterial biomarkers was identified to discriminate between characteristics of the seeds, for example Sphingomonas for improved germination and Brevundimonas for disease resistance. Application of a Bayesian community approach suggested vertical transmission of seed endophytes, where the paternal parent plays a major role and might even determine the germination performance of the offspring. This study contributes to the understanding of seed microbiome assembly and underlines the potential of the microbiome to be implemented in crop breeding and biocontrol programmes.

Bacterial inoculant-assisted phytoremediation affects trace element uptake and metabolite content in Salix atrocinerea

Natural plant-associated microorganisms are of critical importance to plant growth and survival in field conditions under toxic concentrations of trace elements (TE) and these plant-microbial processes can be harnessed to enhance phytoremediation. The total bacterial diversity from grey willow (Salix atrocinerea) on a brownfield heavily-polluted with lead (Pb) and arsenic (As) was studied through pyrosequencing. Culturable bacteria were isolated and in vitro tested for plant growth-promotion (PGP) traits, arsenic (As) tolerance and impact on As speciation. Two of the most promising bacterial strains - the root endophyte Pantoea sp. AV62 and the rhizospheric strain Rhodococcus erythropolis AV96 - were inoculated in field to S. atrocinerea. This bioaugmentation resulted in higher As and Pb concentrations in both, roots and leaves of bacterial-inoculated plants as compared to non-inoculated plants. In consequence, bacterial bioaugmentation also affected parameters related to plant growth, oxidative stress, the levels of phytochelatins and phenylpropanoids, together with the differential expression of genes related to these tolerance mechanisms to TE in leaves. This study extends our understanding about plant-bacterial interactions and provides a solid basis for further bioaugmentation studies aiming to improve TE phytoremediation efficiency and predictability in the field.

Insights into the microbiome assembly during different growth stages and storage of strawberry plants

BACKGROUND

Microbiome assembly was identified as an important factor for plant growth and health, but this process is largely unknown, especially for the fruit microbiome. Therefore, we analyzed strawberry plants of two cultivars by focusing on microbiome tracking during the different growth stages and storage using amplicon sequencing, qPCR, and microscopic approaches.

RESULTS

Strawberry plants carried a highly diverse microbiome, therein the bacterial families Sphingomonadaceae (25%), Pseudomonadaceae (17%), and Burkholderiaceae (11%); and the fungal family Mycosphaerella (45%) were most abundant. All compartments were colonized by high number of bacteria and fungi (10⁷-10¹⁰ marker gene copies per g fresh weight), and were characterized by high microbial diversity (6049 and 1501 ASVs); both were higher for the belowground samples than in the phyllosphere. Compartment type was the main driver of microbial diversity, structure, and abundance (bacterial: 45%; fungal: 61%) when compared to the cultivar (1.6%; 2.2%). Microbiome assembly was strongly divided for belowground habitats and the phyllosphere; only a low proportion of the microbiome was transferred from soil via the rhizosphere to the phyllosphere. During fruit development, we observed the highest rates of microbial transfer from leaves and flowers to ripe fruits, where most of the bacteria occured inside the pulp. In postharvest fruits, microbial diversity decreased while the overall abundance increased. Developing postharvest decay caused by Botrytis cinerea decreased the diversity as well, and induced a reduction of potentially beneficial taxa.

CONCLUSION

Our findings provide insights into microbiome assembly in strawberry plants and highlight the importance of microbe transfer during fruit development and storage with potential implications for food health and safety.

Sodium Alginate–Gelatin Nanoformulations for Encapsulation of Bacillus velezensis and Their Use for Biological Control of Pistachio Gummosis

Biopolymer-based nanocomposites are favorable materials for the encapsulation of biofertilizers and biocontrol agents. In this research, sodium alginate, a widely used natural polymer, was extracted and purified from Macrocystis pyrifera. Its composition was confirmed using ¹H NMR and FTIR analyses, and its molecular weight and mannuronic acid/guluronic acid ratio were obtained. Sodium alginate–gelatin microcapsules enriched with carbon nanotubes and SiO₂ nanoparticles were prepared to encapsulate Bacillus velezensis, and the biological effects of this formulation on the control of pistachio gummosis and growth parameters were investigated. Microscopy examination showed that the microcapsules had quite globular shapes. XRD confirmed the occurrence of an electrostatic interaction when sodium alginate was blended with gelatin. The survival rate of the encapsulated bacteria was about 10⁷ CFU/mL and was maintained after one year of storage. The aim of this study was to achieve a unique formulation containing beneficial bacteria and nanoparticles for the synergistic control of Phytophthora drechsleri.

The microbiome and resistome of apple fruits alter in the post-harvest period

BACKGROUND

A detailed understanding of antimicrobial resistance trends among all human-related environments is key to combat global health threats. In food science, however, the resistome is still little considered. Here, we studied the apple microbiome and resistome from different cultivars (Royal Gala and Braeburn) and sources (freshly harvested in South Africa and exported apples in Austrian supermarkets) by metagenomic approaches, genome reconstruction and isolate sequencing.

RESULTS

All fruits harbor an indigenous, versatile resistome composed of 132 antimicrobial resistance genes (ARGs) encoding for 19 different antibiotic classes. ARGs are partially of clinical relevance and plasmid-encoded; however, their abundance within the metagenomes is very low (≤ 0.03%). Post-harvest, after intercontinental transport, the apple microbiome and resistome was significantly changed independently of the cultivar. In comparison to fresh apples, the post-harvest microbiome is characterized by higher abundance of Enterobacteriales, and a more diversified pool of ARGs, especially associated with multidrug resistance, as well as quinolone, rifampicin, fosfomycin and aminoglycoside resistance. The association of ARGs with metagenome-assembled genomes (MAGs) suggests resistance interconnectivity within the microbiome. Bacterial isolates of the phyla Gammaproteobacteria, Alphaproteobacteria and Actinobacteria served as representatives actively possessing multidrug resistance and ARGs were confirmed by genome sequencing.

CONCLUSION

Our results revealed intrinsic and potentially acquired antimicrobial resistance in apples and strengthen the argument that all plant microbiomes harbor diverse resistance features. Although the apple resistome appears comparatively inconspicuous, we identified storage and transport as potential risk parameters to distribute AMR globally and highlight the need for surveillance of resistance emergence along complex food chains.

Antagonistic activity of endophytic actinobacteria from native potatoes (Solanum tuberosum subsp. tuberosum L.) against Pectobacterium carotovorum subsp. carotovorum and Pectobacterium atrosepticum

BACKGROUND

The native potatoes (Solanum tuberosum subsp. tuberosum L.) grown in Chile (Chiloé) represent a new, unexplored source of endophytes to find potential biological control agents for the prevention of bacterial diseases, like blackleg and soft rot, in potato crops.

RESULT

The objective of this study was the selection of endophytic actinobacteria from native potatoes for antagonistic activity against Pectobacterium carotovorum subsp. carotovorum and Pectobacterium atrosepticum, and their potential to suppress tissue maceration symptoms in potato tubers. This potential was determined through the quorum quenching activity using a Chromobacterium violaceaum ATCC 12472 Wild type (WT) bioassay and its colonization behavior of the potato plant root system (S. tuberosum) by means of the Double labeling of oligonucleotide probes for fluorescence in situ hybridization (DOPE-FISH) targeting technique. The results showed that although Streptomyces sp. TP199 and Streptomyces sp. A2R31 were able to inhibit the growth of the pathogens, only the Streptomyces sp. TP199 isolate inhibited Pectobacterium sp. growth and diminished tissue maceration in tubers (p ≤ 0.05). Streptomyces sp. TP199 had metal-dependent acyl homoserine lactones (AHL) quorum quenching activity in vitro and was able to colonize the root endosphere 10 days after inoculation.

CONCLUSIONS

We concluded that native potatoes from southern Chile possess endophyte actinobacteria that are potential agents for the disease management of soft rot and blackleg.

Evaluation of Bacillus velezensis for Biological Control of Rhizoctonia solani in Bean by Alginate/Gelatin Encapsulation Supplemented with Nanoparticles

Plant growth promoting rhizobacteria (PGPR) are a group of bacteria that can increase plant growth; but due to unfavorable environmental conditions, PGPR are biologically unstable and their survival rates in soil are limited. Therefore, the suitable application of PGPR as a plant growth stimulation is one of the significant challenges in agriculture. This study presents an intelligent formulation based on Bacillus velezensis VRU1 encapsulation enriched with nanoparticles that was able to control Rhizoctonia solani on the bean. The spherical structure of the capsule was observed based on the Scanning Electron Microscope image. Results indicated that with increasing gelatin concentration, the swelling ratio and moisture content were increased; and since the highest encapsulation efficiency and bacterial release were observed at a gelatin concentration of 1.5%, this concentration was considered in mixture with alginate for encapsulation. The application of this formulation which is based on encapsulation and nanotechnology appears to be a promising technique to deliver PGPR in soil and is more effective for plants.

Prospecting Endophytic Bacteria Endowed With Plant Growth Promoting Potential Isolated From Camellia sinensis

Endophytes are well-acknowledged inoculants to promote plant growth, and extensive research has been done in different plants. However, there is a lacuna about the endophytes associated with tea clones and their benefit to promote plant growth. The present study focuses on isolating and characterizing the beneficial endophytic bacteria (EnB) prevalent in commercially important tea clones cultivated in North Eastern India as plant growth promoters. Diversity of culturable EnB microbiome, in vitro traits for plant growth promotion (PGP), and applicability of potent isolates as bioinoculant for in vivo PGP abilities have been assessed in the present study. A total of 106 EnB identified as members of phyla Proteobacteria, Firmicutes, and Actinobacteria were related to 22 different genera and six major clusters. Regarding PGP traits, the percentage of isolates positive for the production of indole acetic acid, phosphate solubilization, nitrogen fixation siderophore, ammonia, and 1-aminocyclopropane-1-carboxylic acid deaminase production were 86.8, 28.3, 78.3, 30.2, 95.3, and 87.7, respectively. In total, 34.0, 52.8, and 17.0% of EnB showed notable production of hydrolytic enzymes like cellulase, protease, and amylase, respectively. Additionally, based on the bonitur score, the top two isolates K96 identified as Stenotrophomonas sp. and M45 identified as Pseudomonas sp. were evaluated for biofilm formation, motility, and in vivo plant growth promoting activity. Results suggested strong biofilm formation and motility in K96 and M45 which may attribute to the colonization of the strains in the plants. Further in vivo plant growth promotion experiment suggested sturdy efficacy of the K96 and M45 as plant growth promoters in nursery condition in commercial tea clones Tocklai vegetative (TV) TV22 and TV26. Thus, this study emphasizes the opportunity of commercialization of the selected isolates for sustainable development of tea and other crops.

Microbial Spectra, Physiological Response and Bioremediation Potential of Phragmites australis for Agricultural Production

Common reed (Phragmites australis) can invade and dominate in its natural habitat which is mainly wetlands. It can tolerate harsh environments as well as remediate polluted and environmental degraded sites such as mine dumps and other polluted wastelands. For this reason, this can be a very critical reed to reclaim wastelands for agricultural use to ensure sustainability. The present review manuscript examined the microbial spectra of P. australis as recorded in various recent studies, its physiological response when growing under stress as well as complementation between rhizosphere microbes and physiological responses which result in plant growth promotion in the process of phytoremediation. Microbes associated with P. australis include Proteobacteria, Bacteriodetes, and Firmicutes, Fusobacteria, Actinobacteria, and Planctomycetes families of bacteria among others. Some of these microbes and arbuscular mycorrhizal fungi have facilitated plant growth and phytoremediation by P. australis. This is worthwhile considering that there are vast areas of polluted and wasted land which require reclamation for agricultural use. Common reed with its associated rhizosphere microbes can be utilized in these land reclamation efforts. This present study suggests further work to identify microbes which when administered to P. australis can stimulate its growth in polluted environments and help in land reclamation efforts for agricultural use.

Culture Separation, Identification and Unique Anti-pathogenic Fungi Capacity of Endophytic Fungi from Gucheng Salvia Miltiorrhiza

BACKGROUND

Salvia miltiorrhiza is a medical herb for human disorders including cardiovascular diseases and cancer. However, the interactions between Salvia miltiorrhiza and its endophytes are largely unknown. The current study aimed at identifying its endophytic fungi and examining their inhibitory effects on anti-pathogenic fungus.

MATERIALS AND METHODS

Distinct species of endophytic fungi were isolated from the roots of Salvia miltiorrhiza, cultured, sequenced, aiming to predict their taxonomical structures. Meanwhile, extracts from each endophytic fungus fermentations were isolated, compared and evaluated on the inhibitory efficacies on five pathological fungi, Cercospora nicotianae, Phoma arachnidicola, Staphylococcus, Phytophthora eggplant, and Rhizoctonia cerealis.

RESULTS

A total of 34 strains of endophytic fungi were obtained from Salvia miltiorrhiza. Among them, SX19 and C. Gloeosporioids exhibited the most effective inhibitions on five pathogenic fungi.

CONCLUSION

The anti-fungal activities of the endophytic fungus from Salvia miltiorrhiza were confirmed for the first time, and this may benefit crop quality and production in the future.

Potato plant spheres and to a lesser extent the soil type influence the proportion and diversity of bacterial isolates with in vitro antagonistic activity towards Ralstonia solanacearum

Ralstonia solanacearum biovar2-race3 (Rs r3b2) is an epidemic soil-borne bacterial phytopathogen causing brown rot disease in potato. In this study, we assessed how three soil types stored at the same field site influenced the proportion and diversity of bacterial isolates with in vitro antagonistic activity towards Rs in bulk soil and different potato plant spheres (rhizosphere, endorhiza and endocaulosphere; ecto- and endosphere of seed and yield tubers). In general, the plate counts observed for each sample type were not significantly different. A total of 96 colonies per sample type was picked and screened for in vitro antagonistic activity against Rs. Antagonists were obtained from all bulk soils and plant spheres with the highest proportion obtained from the endorhiza and endocaulosphere of potato plants. BOX-PCR fingerprints of antagonists showed that some were specific for particular plant spheres independent of the soil type, while others originated from different plant spheres of a particular soil type. The majority of antagonists belonged to Pseudomonas. A high proportion of antagonists produced siderophores, and interestingly antagonists from potato tubers frequently carried multiple antibiotic production genes. Our data showed an enrichment of bacteria with genes or traits potentially involved in biocontrol in the rhizosphere and in endophytic compartments. We report that the proportion and diversity of in vitro antagonists towards Rs isolated from bulk soil and different spheres of potato plants grown under field conditions in three different soil types was mainly shaped by the plant sphere and to a lesser extent by the soil type. Bacteria with antagonistic activity towards Ralstonia solanacearum were isolated from all plant spheres and bulk soils but their proportion was highest in endophytic compartments.

Microbiome Modulation-Toward a Better Understanding of Plant Microbiome Response to Microbial Inoculants

Plant-associated microorganisms are involved in important functions related to growth, performance and health of their hosts. Understanding their modes of action is important for the design of promising microbial inoculants for sustainable agriculture. Plant-associated microorganisms are able to interact with their hosts and often exert specific functions toward potential pathogens; the underlying in vitro interactions are well studied. In contrast, in situ effects of inoculants, and especially their impact on the plant indigenous microbiome was mostly neglected so far. Recently, microbiome research has revolutionized our understanding of plants as coevolved holobionts but also of indigenous microbiome-inoculant interactions. Here we disentangle the effects of microbial inoculants on the indigenous plant microbiome and point out the following types of plant microbiome modulations: (i) transient microbiome shifts, (ii) stabilization or increase of microbial diversity, (iii) stabilization or increase of plant microbiome evenness, (iv) restoration of a dysbiosis/compensation or reduction of a pathogen-induced shift, (v) targeted shifts toward plant beneficial members of the indigenous microbiota, and (vi) suppression of potential pathogens. Therefore, we suggest microbiome modulations as novel and efficient mode of action for microbial inoculants that can also be mediated via the plant.

Characterization of the microbial communities in wheat tissues and rhizosphere soil caused by dwarf bunt of wheat

Dwarf bunt of wheat, which is caused by Tilletia controversa J.G. Kühn, is a soil-borne disease which may lead up to an 80% loss of yield together with degradation of the quality of the wheat flour by production of a fishy smell. In this study, high-throughput sequencing technology was employed to characterize the microbial composition of wheat tissues (roots, spikes, first stem under the ear, and stem base) and rhizosphere soil of wheat varieties that are resistant and susceptible to T. controversa. We observed that the soil fungal community abundance and diversity were higher in resistant varieties than in susceptible varieties in both inoculated and uninoculated wheat, and the abundances of Sordariomycetes and Mortierellomycetes increased in the resistant varieties infected with T. controversa, while the abundances of Dothideomycetes and Bacteroidia increased in the susceptible varieties. Regarding the bacteria present in wheat tissues, the abundances of Chloroflexi, Bacteroidetes, Gemmatimonadetes, Verrucomicrobia and Acidobacteria in the ear and the first stem under the ear were higher than those in other tissues. Our results indicated that the abundances of Sordariomycetes, Mortierellomycetes, Leotiomycetes, Chryseobacterium and Massilia were higher in T. controversa-infected resistant varieties than in their controls, that Dothideomycetes, Bacteroidia, Nocardioides and Pseudomonas showed higher abundances in T. controversa-infected susceptible varieties, and that Curtobacterium, Exiguobacterium, Planococcus, and Pantoea may have higher abundances in both T. controversa-infected susceptible and resistant varieties than in their own controls.

Biochemical and molecular investigation of non-rhizobial endophytic bacteria as potential biofertilisers

This study was performed to isolate non-rhizobial endophytic bacteria from the root nodules of Glycine max (soybean), Vigna radiata (mung bean) and Vigna unguiculata (cowpea). The bacteria were characterized for plant growth promoting properties such as indole acetic acid production, phosphate and zinc solubilisation, nitrogen fixation and hydrogen cyanide production. Phylogenetic identification was performed using the Neighbour-Joining method on16S rRNA gene sequences. The impact of salt tolerant isolates on some properties of wheat cv. Chamran was evaluated by a completely randomised factorial design. Nine isolates having some characteristics related to plant growth promotion were identified as Staphylococcus hominis 7E, Streptomyces sp. 11E, Bacillus sp. 13E, Acinetobacter sp. 19E, from mung bean, Bacillus endophyticus 1E from cowpea, Staphylococcus hominis 9E, Bacillus endophyticus 14E, Brevundimonas sp. 16E and Kocuria sp. 26E from soybean nodules. Isolates 7E and 19E caused maximum growth inhibition of Fusarium on PDA plate. All isolates were able to grow at salinity levels of mixtures containing up to 400 mM of NaCl, CaCl2 and MgCl2, but their growth was inhibited by increasing salinity level. Only the growth of isolate 14E increased at three levels of salinity compared with control. Some isolates, i.e. 7E, 14E, 19E and 26E had higher colony diameter at 45 °C after 48 h of incubation compared to the growth at 30 and 40 °C. Inoculation of soil with isolate 1E and isolate 26E caused to ameliorate salinity stress in wheat and increased the weight of 1000-grains as compared with non-inoculated treatments.

Dissection of plant microbiota and plant-microbiome interactions

Plants rooted in soil have intimate associations with a diverse array of soil microorganisms. While the microbial diversity of soil is enormous, the predominant bacterial phyla associated with plants include Actinobacteria, Bacteroidetes, Firmicutes, Proteobacteria, and Verrucomicrobia. Plants supply nutrient niches for microbes, and microbes support plant functions such as plant growth, development, and stress tolerance. The interdependent interaction between the host plant and its microbes sculpts the plant microbiota. Plant and microbiome interactions are a good model system for understanding the traits in eukaryotic organisms from a holobiont perspective. The holobiont concept of plants, as a consequence of co-evolution of plant host and microbiota, treats plants as a discrete ecological unit assembled with their microbiota. Dissection of plant-microbiome interactions is highly complicated; however, some reductionist approaches are useful, such as the synthetic community method in a gnotobiotic system. Deciphering the interactions between plant and microbiome by this reductionist approach could lead to better elucidation of the functions of microbiota in plants. In addition, analysis of microbial communities' interactions would further enhance our understanding of coordinated plant microbiota functions. Ultimately, better understanding of plantmicrobiome interactions could be translated to improvements in plant productivity.

Development of a Distinct Microbial Community Upon First Season Crop Change in Soils of Long-Term Managed Maize and Rice Fields

The introduction of crop rotation regimes in paddy soils, for example, rice in combination with maize, implements the establishment of new paddy fields to compensate for reduced rice production on existing fields. To study responses of the soil and rhizosphere microbiota upon introduction of a new crop species into continuous cropping agroecosystems, we conducted experiments with soils from adjacent fields where rice and maize were grown successively for more than 30 years. In microcosm experiments, rice and maize plants were cultivated in both soils under the respective plant-required management regime, i.e., rice cultivation under flooded conditions and maize under non-flooded conditions. 16S rRNA gene and fungal ITS region amplicon analysis showed that the soil and rhizosphere microbiota was clearly distinct between soils after long-term rice/maize management. Upon change of the management regime, the bulk soil microbiota became different to both, the former microbial community in the soil and the community being characteristic for the respective type of long-term cropping. Nevertheless, the influence of the soil management history remained clearly visible besides the impact of the new management regime. Similar results were observed for the rhizosphere, though the combined effect of plant species and altered management was even more effective in this compartment compared to the bulk soil. The newly introduced crop plant did not take over characteristic members of the rhizosphere microbiota of the previously cultivated crop; instead, some previously rare taxa became enriched. Thus, the formerly grown crop species did not directly affect the recruitment of microorganisms in the rhizosphere of the following crop species. Further, the results show that the rhizosphere and bulk soil microbiota do not develop straight toward the specific microbiota that is characteristic for a continuous cropping system, but reach a distinct stage upon introduction of a new crop species and new management practices.

Plant growth-promoting bacterial endophytes as biocontrol agents of pre- and post-harvest diseases: Fundamentals, methods of application and future perspectives

Sustainable agriculture requires the recruitment of bacterial agents to control diverse plant diseases such as bacterial endophytes. Bacterial endophytes colonize and inhabit internal plant tissues without causing any apparent damage. Within the plant, these bacteria exert multiple beneficiary effects, including direct stimulation of plant growth by the action of phytohormones or the production of metabolites. However, bacterial endophytes also protect their plant host through biocontrol pathogens or by inducing plant innate immune system. The present work makes a systematic and in-depth review on the current state of endophytic bacterial diversity, their plant colonization strategies, and their potential roles as protective agents against plant diseases during pre- and post-harvest stages of crop productivity. In addition, an exploration of their beneficial effects on sustainable agriculture by reducing/eliminating the use of toxic agrochemicals was conducted. Finally, we propose diverse effective strategies for the application of endophytic bacteria as biological agents during both pre- and post-harvest stages, with the aim of protecting crop plants and their agricultural products.

Optimization of a Method for the Concentration of Genetic Material in Bacterial and Fungal Communities on Fresh Apple Peel Surfaces

Apples are the most consumed fruit in the United States and have recently been shown to exhibit some vulnerability to contamination across the supply chain. It is unclear what role a fruit microbiome analysis may serve in future food safety programs interested in understanding changes in the product and the processing environment. Ultimately, sample integrity is key if any of these approaches are to be employed; low microbial loads on apple surfaces, the inability to sample the entire surface, and inefficiency of removal may act as barriers to achieving high-quality DNA. As such, the objective of this study was to identify a reproducible method to concentrate and quantify bacterial and fungal DNA from fresh apple surfaces. Five methods were evaluated: two variations of wash solutions for bath sonication, wash filtration, epidermis excision, and surface swabbing. Epidermis excision returned the highest mean DNA quantities, followed by the sonicated washes and wash filtration. Surface swabbing was consistently below the limit of detection. Based on the quantity of host DNA contamination in surface excision, the sonicated wash solution containing a surfactant presents the greatest opportunity for consistent, high-yielding DNA recovery from the entire apple surface.

The unexplored bacterial lifestyle on leaf surface

Social interactions impact microbial communities and these relationships are mediated by small molecules. The chemical ecology of bacteria on the phylloplane environment is still little explored. The harsh environmental conditions found on leaf surface require high metabolic performances of the bacteria in order to survive. That is interesting both for scientific fields of prospecting natural molecules and for the ecological studies. Important queries about the bacterial lifestyle on leaf surface remain not fully comprehended. Does the hostility of the environment increase the populations' cellular altruism by the production of molecules, which can benefit the whole community? Or does the reverse occur and the production of molecules related to competition between species is increased? Does the phylogenetic distance between the bacterial populations influence the chemical profile during social interactions? Do phylogenetically related bacteria tend to cooperate more than the distant ones? The phylloplane contains high levels of yet uncultivated microorganisms, and understanding the molecular basis of the social networks on this habitat is crucial to gain new insights on the ecology of the mysterious community members due to interspecies molecular dependence. Here, we review and discuss what is known about bacterial social interactions and their chemical lifestyle on leaf surface.

Crop management system and carrot genotype affect endophyte composition and Alternaria dauci suppression

Managing pests in carrot production is challenging. Endophytic microbes have been demonstrated to improve the health and productivity of many crops, but factors affecting endophyte dynamics in carrot is still not well understood. The goal of this study was to determine how crop management system and carrot genotype interact to affect the composition and potential of endophytes to mitigate disease caused by Alternaria dauci, an important carrot pathogen. Twenty-eight unique isolates were collected from the taproots of nine diverse genotypes of carrot grown in a long-term trial comparing organic and conventional management. Antagonistic activity was quantified using an in vitro assay, and potential for individual isolates to mitigate disease was evaluated in greenhouse trials using two carrot cultivars. Results confirm that carrot taproots are colonized by an abundant and diverse assortment of bacteria and fungi representing at least distinct 13 genera. Soils in the organic system had greater total organic matter, microbial biomass and activity than the conventional system and endophyte composition in taproots grown in this system were more abundant and diverse, and had greater antagonistic activity. Carrot genotype also affected endophyte abundance as well as potential for individual isolates to affect seed germination, seedling growth and tolerance to A. dauci. The benefits of endophytes on carrot growth were greatest when plants were subject to A. dauci stress, highlighting the importance of environmental conditions in the functional role of endophytes. Results of this study provide evidence that endophytes can play an important role in improving carrot performance and mediating resistance to A. dauci, and it may someday be possible to select for these beneficial plant-microbial relationships in carrot breeding programs. Implementing soil-building practices commonly used in organic farming systems has potential to promote these beneficial relationships and improve the health and productivity of carrot crops.

Plant-microbe Interactions for Sustainable Agriculture in the Post-genomic Era

Plant-microbe interactions are both symbiotic and antagonistic, and the knowledge of both these interactions is equally important for the progress of agricultural practice and produce. This review gives an insight into the recent advances that have been made in the plant-microbe interaction study in the post-genomic era and the application of those for enhancing agricultural production. Adoption of next-generation sequencing (NGS) and marker assisted selection of resistant genes in plants, equipped with cloning and recombination techniques, has progressed the techniques for the development of resistant plant varieties by leaps and bounds. Genome-wide association studies (GWAS) of both plants and microbes have made the selection of desirable traits in plants and manipulation of the genomes of both plants and microbes effortless and less time-consuming. Stress tolerance in plants has been shown to be accentuated by association of certain microorganisms with the plant, the study and application of the same have helped develop stress-resistant varieties of crops. Beneficial microbes associated with plants are being extensively used for the development of microbial consortia that can be applied directly to the plants or the soil. Next-generation sequencing approaches have made it possible to identify the function of microbes associated in the plant microbiome that are both culturable and non-culturable, thus opening up new doors and possibilities for the use of these huge resources of microbes that can have a potential impact on agriculture.

Midgut microbiota diversity of potato tuber moth associated with potato tissue consumed

Background

The potato tuber moth (PTM), Phthorimaea operculella (Zeller), is a worldwide pest that feeds on both the leaves and tubers of potato plants. PTM larvae can digest leaves, or tubers, resulting in serious damage to potato plants in the field and potato tubers in storage. To understand how midgut bacterial diversity is influenced by the consumption of these two tissue types, the symbiotic bacteria in the potato-feeding PTM midgut and the endophytic bacteria of potato tissues were analyzed.

Results

At the genus level, the bacterial community composition in the PTM midgut was influenced by the tissues consumed, owing to their different nutrient contents. Escherichia_Shigella and Enterobacter were the most dominant genera in the midgut of leaf-feeding and tuber-feeding PTMs, respectively. Interestingly, even though only present in low abundance in leaves and tubers, Escherichia_Shigella were dominantly distributed only in the midgut of leaf-feeding PTMs, indicating that specific accumulation of these genera have occurred by feeding on leaves. Moreover, Enterobacter, the most dominant genus in the midgut of tuber-feeding PTMs, was undetectable in all potato tissues, indicating it is gut-specific origin and tuber feeding-specific accumulation. Both Escherichia_Shigella and Enterobacter abundances were positively correlated with the dominant contents of potato leaves and tubers, respectively.

Conclusions

Enrichment of specific PTM midgut bacterial communities was related to different nutrient levels in different tissues consumed by the insect, which in turn influenced host utilization. We provide evidence that a portion of the intestinal microbes of PTMs may be derived from potato endophytic bacteria and improve the understanding of the relationship between potato endophytic bacteria and the gut microbiota of PTMs, which may offer support for integrated management of this worldwide pest.

Impact of plant genotype and plant habitat in shaping bacterial pathobiome: a comparative study in olive tree

Plant-inhabiting microorganisms interact directly with each other affecting disease progression. However, the role of host plant and plant habitat in shaping pathobiome composition and their implication for host susceptibility/resistance to a particular disease are currently unknown. For the elucidation of these questions, both epiphytic and endophytic bacterial communities, present in asymptomatic and symptomatic twigs from olive cultivars displaying different susceptibilities to olive knot (OK) disease, were investigated using culturing methods. OK disease was the main driver of the bacterial community, causing changes on their diversity, abundance and composition. OK disease effect was most notorious on OK-susceptible cultivar and when considering the endophytic communities. Plant habitat (epiphytes vs. endophytes) also contributed to the bacterial community assembling, in particular on symptomatic twigs (knots) of OK-susceptible cultivar. In contrast, host cultivar had little effect on the bacterial community composition, but OK-symptomatic twigs (knots) revealed to be more affected by this driver. Overall, the pathobiome seems to result from an intricate interaction between the pathogen, the resident bacteria, and the plant host. Specific bacterial genera were associated to the presence or absence of OK disease in each cultivar. Their ability to trigger and/or suppress disease should be studied in the future.

In Planta Colonization and Role of T6SS in Two Rice Kosakonia Endophytes

Endophytes live inside plants and are often beneficial. Kosakonia is a novel bacterial genus that includes many diazotrophic plant-associated isolates. Plant-bacteria studies on two rice endophytic Kosakonia beneficial strains were performed, including comparative genomics, secretome profiling, in planta tests, and a field release trial. The strains are efficient rhizoplane and root endosphere colonizers and localized in the root cortex. Secretomics revealed 144 putative secreted proteins, including type VI secretory system (T6SS) proteins. A Kosakonia T6SS genomic knock-out mutant showed a significant decrease in rhizoplane and endosphere colonization ability. A field trial using rice seed inoculated with Kosakonia spp. showed no effect on plant growth promotion upon nitrogen stress and microbiome studies revealed that Kosakonia spp. were significantly more present in the inoculated rice. Comparative genomics indicated that several protein domains were enriched in plant-associated Kosakonia spp. This study highlights that Kosakonia is an important, recently classified genus involved in plant-bacteria interaction.

Understanding the Impact of Cultivar, Seed Origin, and Substrate on Bacterial Diversity of the Sugar Beet Rhizosphere and Suppression of Soil-Borne Pathogens

The rhizosphere microbiome is crucial for plant health, especially for preventing roots from being infected by soil-borne pathogens. Microbiota-mediated pathogen response in the soil-root interface may hold the key for microbiome-based control strategies of phytopathogens. We studied the pathosystem sugar beet-late sugar beet root rot caused by Rhizoctonia solani in an integrative design of combining in vitro and in vivo (greenhouse and field) trials. We used five different cultivars originating from two propagation sites (France, Italy) with different degrees of susceptibility towards R. solani (two susceptible, one moderately tolerant and two cultivars with partial resistance). Analyzing bacterial communities in seeds and roots grown under different conditions by 16S rRNA amplicon sequencing, we found site-, cultivar-, and microhabitat-specific amplicon sequences variants (ASV) as well as a seed core microbiome shared between all sugar beet cultivars (121 ASVs representing 80%-91% relative abundance). In general, cultivar-specific differences in the bacterial communities were more pronounced in seeds than in roots. Seeds of Rhizoctonia-tolerant cultivars contain a higher relative abundance of the genera Paenibacillus, Kosakonia, and Enterobacter, while Gaiellales, Rhizobiales, and Kosakonia were enhanced in responsive rhizospheres. These results indicate a correlation between bacterial seed endophytes and Rhizoctonia-tolerant cultivars. Root communities are mainly substrate-derived but also comprise taxa exclusively derived from seeds. Interestingly, the signature of Pseudomonas poae Re*1-1-14, a well-studied sugar-beet specific biocontrol agent, was frequently found and in higher relative abundances in Rhizoctonia-tolerant than in susceptible cultivars. For microbiome management, we introduced microbial inoculants (consortia) and microbiome transplants (vermicompost) in greenhouse and field trials; both can modulate the rhizosphere and mediate tolerance towards late sugar beet root rot. Both, seeds and soil, provide specific beneficial bacteria for rhizosphere assembly and microbiota-mediated pathogen tolerance. This can be translated into microbiome management strategies for plant and ecosystem health.

The ecological role of bacterial seed endophytes associated with wild cabbage in the United Kingdom

Endophytic bacteria are known for their ability in promoting plant growth and defense against biotic and abiotic stress. However, very little is known about the microbial endophytes living in the spermosphere. Here, we isolated bacteria from the seeds of five different populations of wild cabbage (Brassica oleracea L) that grow within 15 km of each other along the Dorset coast in the UK. The seeds of each plant population contained a unique microbiome. Sequencing of the 16S rRNA genes revealed that these bacteria belong to three different phyla (Actinobacteria, Firmicutes, and Proteobacteria). Isolated endophytic bacteria were grown in monocultures or mixtures and the effects of bacterial volatile organic compounds (VOCs) on the growth and development on B. oleracea and on resistance against a insect herbivore was evaluated. Our results reveal that the VOCs emitted by the endophytic bacteria had a profound effect on plant development but only a minor effect on resistance against an herbivore of B. oleracea. Plants exposed to bacterial VOCs showed faster seed germination and seedling development. Furthermore, seed endophytic bacteria exhibited activity via volatiles against the plant pathogen F. culmorum. Hence, our results illustrate the ecological importance of the bacterial seed microbiome for host plant health and development.

Cultivar-Dependent Variation of the Cotton Rhizosphere and Endosphere Microbiome Under Field Conditions

Verticillium wilt caused by Verticillium dahliae is a common soil-borne disease worldwide, affecting many economically important crop species. Soil microbes can influence plant disease development. We investigated rhizosphere and endosphere microbiomes in relation to cotton cultivars with differential susceptibility to Verticillium wilt. Soil samples from nine cotton cultivars were assessed for the density of V. dahliae microsclerotia; plants were assessed for disease development. We used amplicon sequencing to profile both bacterial and fungal communities. Unlike wilt severity, wilt inoculum density did not differ significantly among resistant and susceptible cultivars. Overall, there were no significant association of alpha diversity indices with wilt susceptibility. In contrast, there were clear differences in the overall rhizosphere and endosphere microbial communities, particularly bacteria, between resistant and susceptible cultivars. Many rhizosphere and endosphere microbial groups differed in their relative abundance between resistant and susceptible cultivars. These operational taxonomic units included several well-known taxonomy groups containing beneficial microbes, such as Bacillales, Pseudomonadales, Rhizobiales, and Trichoderma, which were higher in their relative abundance in resistant cultivars. Greenhouse studies with sterilized soil supported that beneficial microbes in the rhizosphere contribute to reduced wilt development. These findings suggested that specific rhizosphere and endosphere microbes may contribute to cotton resistance to V. dahliae.

Deciphering the microbiome shift during fermentation of medicinal plants

The importance of the human-microbiome relationship for positive health outcomes has become more apparent over the last decade. Influencing the gut microbiome via modification of diet represents a possibility of maintaining a healthy gut flora. Fermented food and lactic acid bacteria (LAB) display a preventive way to inhibit microbial dysbioses and diseases, but their ecology on plants is poorly understood. We characterized the microbiome of medicinal plants (Matricaria chamomilla L. and Calendula officinalis L.) using 16S rRNA gene profiling from leaves that were fermented over a six-week time course. The unfermented samples were characterized by a distinct phyllosphere microbiome, while the endosphere revealed a high similarity. During fermentation, significant microbial shifts were observed, whereby LAB were enhanced in all approaches but never numerically dominated. Among the LAB, Enterococcaceae were identified as the most dominant family in both plants. M. chamomilla community had higher relative abundances of Lactobacillaceae and Carnobacteriaceae, while C. officinalis showed a higher presence of Leuconostocaceae and Streptococcaceae. The natural leaf microbiome and the indigenous LAB communities of field-grown Asteraceae medicinal plants are plant-specific and habitat-specific and are subjected to significant shifts during fermentation. Leaf surfaces as well as leaf endospheres were identified as sources for biopreservative LAB.

Genetic Potential of the Biocontrol Agent Pseudomonas brassicacearum (Formerly P. trivialis) 3Re2-7 Unraveled by Genome Sequencing and Mining, Comparative Genomics and Transcriptomics

The genus Pseudomonas comprises many known plant-associated microbes with plant growth promotion and disease suppression properties. Genome-based studies allow the prediction of the underlying mechanisms using genome mining tools and the analysis of the genes unique for a strain by implementing comparative genomics. Here, we provide the genome sequence of the strain Pseudomonas brassicacearum 3Re2-7, formerly known as P. trivialis and P. reactans, elucidate its revised taxonomic classification, experimentally verify the gene predictions by transcriptome sequencing, describe its genetic biocontrol potential and contextualize it to other known Pseudomonas biocontrol agents. The P. brassicacearum 3Re2-7 genome comprises a circular chromosome with a size of 6,738,544 bp and a GC-content of 60.83%. 6267 genes were annotated, of which 6113 were shown to be transcribed in rich medium and/or in the presence of Rhizoctonia solani. Genome mining identified genes related to biocontrol traits such as secondary metabolite and siderophore biosynthesis, plant growth promotion, inorganic phosphate solubilization, biosynthesis of lipo- and exopolysaccharides, exoproteases, volatiles and detoxification. Core genome analysis revealed, that the 3Re2-7 genome exhibits a high collinearity with the representative genome for the species, P. brassicacearum subsp. brassicacearum NFM421. Comparative genomics allowed the identification of 105 specific genes and revealed gene clusters that might encode specialized biocontrol mechanisms of strain 3Re2-7. Moreover, we captured the transcriptome of P. brassicacearum 3Re2-7, confirming the transcription of the predicted biocontrol-related genes. The gene clusters coding for 2,4-diacetylphloroglucinol (phlABCDEFGH) and hydrogen cyanide (hcnABC) were shown to be highly transcribed. Further genes predicted to encode putative alginate production enzymes, a pyrroloquinoline quinone precursor peptide PqqA and a matrixin family metalloprotease were also found to be highly transcribed. With this study, we provide a basis to further characterize the mechanisms for biocontrol in Pseudomonas species, towards a sustainable and safe application of P. brassicacearum biocontrol agents.

Identification of endophytic bacteria in medicinal plants and their antifungal activities against food spoilage fungi

Endophytes are fungi or bacteria living in the intracellular parts of the plants. In this study, 12 medicinal plants were examined for the presence of endophytic bacteria. Antifungal activities of the isolates were determined against Aspergillus flavus PTCC 5006, Penicillium citrinum PTCC 5304, Aspergillus fumigatus PTCC 5006, Fusarium oxysporum MTCC 284, and Rhizopus stolonifer. In order to determine the metabolites characteristics of these isolates, catalase and proteolytic enzyme treatments were assessed. Moreover, approximate molecular weights of the antifungal substance were measured by fractionation method and the volatile compounds were determined by using GC-mass spectroscopy. Finally, 16s rRNA gene sequencing confirmed the strain of the bacteria. Twenty-one endophytic bacteria, out of a total of 82 isolates, showed antifungal activities against all five spoilage fungi. The results of the PCR assay revealed two species: Bacillus pumilus and B. safensis. Proteolytic enzyme activities and the fractionation of the supernatants proved that more than one compound was responsible for the antifungal activities. This compound could be proteins, peptides, and other low-molecular compounds, such as Butanal, 3-methyl-, Propene, 2-butene, 2-heptanone, 6-methyl-5-methylene-, and 6-oxabicyclo[3.1.0] hexane, which all were identified in the headspace of the GC-mass spectroscopy.